By Gabriela Ríos Ríos, SLS LLM and CLB Student Fellow, 2025

This is the first of a three-part blog post. 

“After decades of concentrated efforts, we are finally learning how to harness natural processes honed over millions of years of evolution to translate our unparalleled ability to read the genome into a new opportunity to write it and to correct the grave mistakes that turn it against us”

-Euan Angus Ashley[1]

Introduction: A scientific inflection point

In 1959, French geneticist Jérôme Lejeune made a landmark discovery – Down syndrome was caused by the presence of an extra copy of chromosome 21. For over six decades since this revelation, our approach to this most common chromosomal disorder has been primarily supportive: therapies to address symptoms, early interventions to maximize development, and social inclusion to improve quality of life. Despite tremendous advances in understanding the molecular basis of the condition, the fundamental problem – that extra chromosome – remained untouchable. We could detect it, study it, even track how it disrupts normal development, but we could not remove it. Until now.

In a groundbreaking study published in PNAS Nexus in early 2025, Hashizume et al.[2] demonstrate a technique that could selectively eliminates the extra chromosome in trisomy 21. Using a sophisticated application of CRISPR-Cas9 gene editing technology, the researchers achieved something once thought impossible: targeted removal of an entire chromosome while leaving the necessary pair intact. This approach corrects the underlying genetic imbalance, reversing cellular abnormalities and restoring normal gene expression patterns in laboratory-grown cells.

Although this work took place only in human cell lines and not in living people, or human embryos, its possible implications are profound. Rather than treatments that address individual symptoms, this research opens the door to therapy that could potentially address the genetic root cause of Down syndrome. The technique still requires refinement but represents a watershed moment in genetic medicine: the first successful demonstration of precise, allele-specific chromosome elimination in human trisomy 21 cells.

Yet as with many scientific breakthroughs, this advance raises as many questions as it answers. If we can remove the extra chromosome causing Down syndrome, should we? When would such intervention be appropriate—in embryos, children, or adults? Who decides which genetic conditions merit correction? How do we balance medical benefit against the risks of unintended genomic damage and the value of disability?

This three-part blog post examines the remarkable science behind this chromosome-level editing technique and the complex ethical questions it raises. The first blog post will be dedicated to understanding the science: the technique proposed by Hashizume et al. to eliminate the third copy of the 21^st chromosome that causes down syndrome and how the researchers achieved allele-specific targeting. The second blog post will be dedicated to analyzing the risks and limitations; and the third blog post will dive into the difficult ethical questions it raises if the technique advances to clinical application and briefly assess the legal landscape governing such interventions across jurisdictions.

1. Down Syndrome and its management

Down syndrome occurs when an individual carries three copies of chromosome 21 rather than the typical two. The presence of a third chromosome leads to an excess of genetic material that disrupts normal cellular function and development.

Various medical issues have been associated with Down syndrome, such as congenital heart defects (40-50% of children) that range in severity, gastrointestinal problems, immune system dysfunction and infections, increased risk of leukemia and other blood disorders, thyroid disorders, hearing problems (75% of Down children experience some degree of hearing loss) and vision problems, neurological and cognitive impairment, among others[3].

The initial approach to patients with Down syndrome has been medical support. However, as science has advanced, and particularly since the emergence of prenatal genetic testing, parents have had the possibility of terminating the pregnancy once a Down syndrome diagnosis has been given. And, if they are using in vitro fertilization, they have the further option of using preimplantation genetic diagnosis to avoid transferring a trisomy 21 embryo for possible implantation, pregnancy, and birth. Available research on the subject shows significant variation per country in termination rates for prenatally diagnosed cases: Iceland near 100% termination rates; Spain, France and Germany 96%; Italy 93%; England and Wales 76%[4], and 67% in the US[5]^/[6]. The data varies significantly across different sources, but it has raised concerns among the bioethics community.

2. The science – Understanding CRISPR-Based chromosome elimination

The Hashizume study implements a molecular strategy to eliminate the extra chromosome in trisomy 21 cells. It introduces a paradigm shift in chromosomal disorder therapeutics by combining allele-specific CRISPR-Cas9 targeting (precision scissors and targeting) with DNA repair pathway modulation (sabotage of repair crews) to achieve functional trisomy rescue.

Step 1: “Fingerprinting” the Chromosome

The innovation in Hashizume’s study relies on a crucial insight: although the three copies of chromosome 21 look nearly identical, they contain subtle genetic differences that can be exploited.

Using a technique called haplotype phasing, the researchers first “fingerprinted” each chromosome to identify which was inherited from the father (P) and which from the mother (M1 and M2). After determining that the M2 chromosome was the safest to remove, they designed a CRISPR-Cas9 system that could recognize and cut only this specific chromosome.

What makes this approach revolutionary is its precision. Unlike previous “allele-nonspecific” (ANS) methods that indiscriminately cut all three chromosomes, the “allele-specific” (AS) approach targets only the extra chromosome. This distinction is critical, with this technique, the CRISPR system cuts all three chromosomes, and it overwhelms the cell’s repair mechanisms and frequently leads to cell death (87.3% of cells died). In contrast, the AS approach achieved both better survival rates (57%) and higher chromosome elimination rates (13.1% versus 6-8% for ANS methods).

Step 2: Designing Precision-Guided Scissors (multiplexed CRISPR cuts)

The mechanism works like molecular surgery: CRISPR-Cas9 creates 13 strategic cuts along the M2 chromosome, essentially shredding it into fragments. The scientists created 12 guide RNAs, molecules directing the Cas9 protein to the M2 chromosome to cut it. A considerable percentage, approximately 33%, of those gRNAs were successful. Thanks to multiple cuts in the targeted chromosome, it is impossible for the cell to repair the damage.

Step 3: DNA repair inhibition

The researchers enhanced this effect by temporarily suppressing key DNA repair genes (POLQ and LIG4), preventing the cell from stitching the broken chromosome back together. During subsequent cell division, these chromosome fragments fail to properly segregate and are ultimately lost, effectively removing the extra chromosome and restoring.

The scientists then blocked the cell repair mechanisms (NHEJ and MMEJ pathways) by temporarily blocking them with siRNA (a silencing molecule) which doubled the success rate of chromosome loss.

Key Result	Allele-Specific (AS) Method	Non-Specific (ANS) Method
Chromosomal elimination rate	13.1%	6-8%
Cell survival rate	57%	12-7%
Off-target DNA damage	Minimal (5-6 errors)	Widespread

To verify their success, the team conducted comprehensive genetic analyses, confirming that the eliminated chromosome was indeed the targeted M2 in every case. More importantly, cells that lost this chromosome showed dramatic improvements: gene expression patterns normalized, cellular stress decreased, and proliferation rates increased—effectively reversing the cellular manifestations of Down syndrome.

[1] Euan Angus Ashley, The Genome Odyssey: Medical Mysteries and the Incredible Quest to Solve Them, 1st ed. (Celadon Books, 2021), https://us.macmillan.com/books/9781250792150/thegenomeodyssey/.

[2] Ryotaro Hashizume et al., “Trisomic Rescue via Allele-Specific Multiple Chromosome Cleavage Using CRISPR-Cas9 in Trisomy 21 Cells,” PNAS Nexus 4, no. 2 (2025): pgaf022, https://doi.org/10.1093/pnasnexus/pgaf022.

[3] “Down Syndrome – Symptoms and Causes,” Mayo Clinic, accessed April 17, 2025, https://www.mayoclinic.org/diseases-conditions/down-syndrome/symptoms-causes/syc-20355977.

[4] PA Boyd et al., “Survey of Prenatal Screening Policies in Europe for Structural Malformations and Chromosome Anomalies, and Their Impact on Detection and Termination Rates for Neural Tube Defects and Down’s Syndrome,” Bjog 115, no. 6 (2008): 689–96, https://doi.org/10.1111/j.1471-0528.2008.01700.x.

[5] “In Iceland, Almost All Diagnosed Down Syndrome Pregnancies Are Aborted after Prenatal Testing. Some Bioethics Experts Are Concerned – ABC News,” accessed April 17, 2025, https://amp.abc.net.au/article/103781058.

[6] Gert de Graaf et al., “Estimates of the Live Births, Natural Losses, and Elective Terminations with Down Syndrome in the United States,” American Journal of Medical Genetics Part A 167, no. 4 (2015): 756–67, https://doi.org/10.1002/ajmg.a.37001.